HLA-DQB1 genotyping with simple automated DNA sequencing and single-strand conformation polymorphism analysis

Accurate human leukocyte antigen (HLA) typing is important for matching donors and recipients of bone marrow transplantation. Because HLA is highly polymorphic, HLA genotyping is also a valuable tool in forensic identification of humans. The primary objective of this study was to establish a simple, rapid, and economic HLA analysis system suitable for use in forensic applications.

We used the primer pair DB130 and CH29 to amplify the HLA class II DQB1 gene by polymerase chain reaction (PCR). The nucleotide sequences of the PCR products were analyzed with an ABI Prism 377 automatic DNA sequencer, with the aid of its systematic analytical procedure. Some genotypes were confirmed by single-strand conformation polymorphism (SSCP) analysis.

We identified 15 alleles and 37 genotypes from 86 Taiwanese subjects. The most frequent allele was 03011 (27.9%) and the most frequent genotype was 03011/03011 (15.1%). Statistical analysis showed that the allelic diversity was 0.862 and the power of discrimination was 0.948.

The results of this study indicate that the combined use of automated sequencing with only one primer pair and SSCP provides a simple, rapid, and economic tool for analyzing the DQB1 gene. Compared with other sequencing methods that use a set of multiple primers, this method has two advantages. First, it is simpler and faster, because the HLAB1 genotype can be determined in a single PCR reaction. Second, the use of only one primer set obviates the need for preferential annealing of any one primer set.